Hi Brenton,
Add a specific atom, at which you want the label, to the selection. You can
pick one to get to know its name.
Cheers,
Tsjerk
On Mon, Apr 6, 2015 at 10:03 PM, Brenton Horne <brentonho...@ymail.com>
wrote:
> Hi,
>
> I have skimmed the Label <http://pymolwiki.org/index.php/Label> page on
> PyMOL Wiki and it only appears to give examples about how to label specific
> atoms and not whole ligands or residues. See I'd like to label residue 403
> as "Ser403", ceftaroline's open form (het ID AI8) as "Open CFT" and
> ceftaroline (het ID 1W8) as "CFT" in the structure that has the PDB ID
> 3ZG0. I presently have the PyMOL code:
>
> delete all
> load 3zg0.pdb1
> hide
> show cartoon
>
> # Colouring secondary structure
> set_color blues, [0.0196078,0.7607843,0.7607843]
>
> color red, ss h
> color yellow, ss s
> color blues, ss l+""
>
> show sticks, r. 1w8
> label (r. 1w8), "CFT"
> show sticks, r. ai8
> label (r. ai8), "open-chain CFT"
> show sticks, r. mur
>
> show sticks, resi 403
> color green, resi 403
> label (resi 403), "Ser403"
> h_add
> set valence, 0.2
>
>
> set_color orange, [1, 0.5, 0]
> set_color fluorine, [0.5625,0.875,0.3125]
> set_color chlorine, [0.12109375,0.9375,0.12109375]
> set_color sulfur, [1,1,0.18750]
>
> # Colouring elements
> #color black, elem c and resi 69 and not name c+n+o
> color black, elem c and organic
>
> #color blue, elem n and resi 69 and not name c+n+o
> color blue, elem n and organic
>
> #color white, elem h and resi 69 and not name c+n+o
> color white, elem h and organic
>
> #color red, elem o and resi 69 and not name c+n+o
> color red, elem o and organic
>
> #color orange, elem p and resi 69 and not name c+n+o
> color orange, elem p and organic
>
> #color fluorine, elem f and resi 69 and not name c+n+o
> color fluorine, elem f and organic
>
> #color chlorine, elem cl and resi 69 and not name c+n+o
> color chlorine, elem cl and organic
>
> color sulfur, elem s and organic
>
> # Colour backgrond white
> bg_color white
>
> remove solvent
>
> With the relevant code indented. The result was
> http://i.imgur.com/lXoZmQA.png. The problem, however, is that as you can
> see in this image this code doesn't give just a single, individual label
> for each of the two ligands and serine 403, rather it appears to label each
> individual atom in each of these three molecules of interest. So my
> question is how do I get just a single label for each molecule of interest
> and not for every atom inside these molecules.
>
> Thanks for your time,
> Brenton
>
>
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live
> exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
> event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Tsjerk A. Wassenaar, Ph.D.
------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
